Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

Abstract

Hi-C experiments study how genomes fold in 3D, generating contact maps containing features as small as 20bp and as large as 200-Mb. Here we introduce Juicebox, a tool for exploring Hi-C and other contact map data. Juicebox allows users to zoom in and out of Hi-C maps interactively, just as a user of Google Earth might zoom in and out of a geographic map. Maps can be compared to one another, or to 1D tracks or 2D feature sets.

The Juicebox Assembly Tools module facilitatesde novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000

“…Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al 2017). Here, we introduce "Assembly Tools," a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly.…”

“…Recently, we introduced Juicebox, a set of tools that facilitate the visual exploration of Hi-C heatmaps across a wide range of scales (Durand, Robinson et al 2016). Here, we introduce "Assembly Tools" (see Fig.…”

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

“…For the GM12878 cell line, we used the samples GSM1551574 and GSM1551575; for K562, we used the samples GSM1551620 and GSM1551623. Hi-C matrices were normalized using the VC-squared method available in the Juicebox tool (Durand et al 2016). For each condition, inter-sample normalization was performed using the MA-plot approach (described below).…”

“…For data visualization, we used the R Environment for Statistical Computing (R Core Team 2016) for the generation of Figure 6 and Supplemental Figure S6, we used the Juicebox tool (Durand et al 2016). …”

Visualization of Biomedical Data

“…Thus, tailored visualization methods are being developed, currently based around three alternative views. In one, Hi-C data are shown as a contact matrix (Figure 4c), allowing for high data density and a clear overview (38) but making it difficult to overlay other genomic features. A pyramidal layout (Figure 4d) addresses this issue (39) but makes it harder to see contacting regions.…”